Thank you everyone for such quick and helpful responses. So I just want to make 
sure I understand all of this correctly since it is my first real experience with jar 
files. I imagine my process of getting from my project to executable application as 
follows:

1.) As discussed in the PDF support doc, going into the proper directory in mason 
and running the unix command:   make jar 

2a.) Taking the resulting jar file and using Launch4j (since it is open source) to 
create an executable.

2b.) Making sure to add lib/* to the "Classpath" in the respective tab in the 
Launch4j GUI when making the executable.

Is this right? I'm mostly concerned about step 1 as I don't know if this is the right 
way to make a jar to be used in an executable application. If it is, in which folder 
do I run make jar? The PDF was not very clear on that.

Once again, thank you so much,
Steve Kraska